Enzyme P1 Lecture Notes PDF

Enzymes M.Pichkhaia  Enzymes-part 1 Textbook-Lippincott Illustrated Reviews Biochemistry, 8th edition, 2021 Chapter 5 -Enzymes Pages: 165-202 Topics which have to be learned 1. Classification of enzymes 2. Enzymes and their properties 3. Holoenzymes, apoenzymes, cofactors,...

Enzymes M.Pichkhaia  Enzymes-part 1 Textbook-Lippincott Illustrated Reviews Biochemistry, 8th edition, 2021 Chapter 5 -Enzymes Pages: 165-202 Topics which have to be learned 1. Classification of enzymes 2. Enzymes and their properties 3. Holoenzymes, apoenzymes, cofactors, and coenzymes 4. Mechanism of enzyme action 5. Kinetics of chemical reactions 6. Factors affecting enzyme activity:Substrate concentration, pH, Temperature  How to define an enzyme? Enzymes are biologically active proteins that accelerate the breakdown of food that is eaten. Enzymes are biological catalysts. They accelerate reactions, but are not consumed or changed in reactions. They are involved in all processes essential for life such as DNA replication and transcription, protein synthesis, metabolism and signal transduction, etc.  How to define an enzyme? Bee-enzyme Flower- substrate Product- honey Oxidoreductases Transferases Hydrolases Lyases Isomerases Ligases  Isoenzymes Isoenzymes are enzymes that catalyze the same reaction but differ in their amino acid sequence and, therefore, in many of their properties. Tissues contain characteristic isozymes or mixtures of isozymes. Enzymes, such as lactate dehydrogenase and creatine kinase (CK), differ fom one tissue to another. 1. Lactate dehydrogennt contains four subunits. Each subunit may be either of the heart (H) or the muscle(M) type. Five isozymes exist (HHHH, HHHM, HHMM, HMMM, and MMMM). 2. CK contains two subunits. Each subunit may be either of the muscle (M) or the brain (B) type. Three fsozymes exist (MM, MB, and BB). The MB fraction is most prevalent in heart muscle.  Active Site Enzyme molecules contain a special pocket or cleft called the active site. The active site, formed by folding of the protein, contains amino acid side chains that participate in substrate binding and catalysis The substrate binds the enzyme noncovalently, forming an enzyme– substrate (ES) complex  Substrate-Binding sites Enzyme specificity (the enzyme’s ability to react with just one substrate) results from the three-dimensional arrangement of specific amino acid residues in the enzyme that form binding sites for the substrates and activate the substrates during the course of the reaction. The “lock-and-key and the “induced-fit” models for substrate binding describe two aspects of the binding interaction between the enzyme and substrate.  Enzyme–substrate models Enzyme is flexible, and after substrates bind to the enzyme , the conformation of the protein changes so that a stable binary complex forms. Binding site for substrate on the enzyme is a rigid entity and only a compound with a particular shape will fit.  Cofactors and Coenzymes Many enzymes don’t work optimally, or even at all, unless bound to other non-protein helper molecules called cofactors. These may be attached temporarily to the enzyme through ionic or hydrogen bonds, or permanently through stronger covalent bonds. Coenzymes are a subset of cofactors that are organic (carbon-based) molecules. The most common sources of coenzymes are dietary vitamins. Some vitamins are precursors to coenzymes and others act directly as coenzymes. Enzymes with covalently or noncovalently bound coenzymes are referred to as holoenzymes. A holoenzyme without a coenzyme is termed an apoenzyme. Cofactors and Coenzymes  GENERAL CONCEPTS OF ENZYME MECHANISMS Most chemical reactions can be described as the conversion of a substrate to a product (A~ B). This process often includes a transition state (A - B), an intermediate form between substrate and product. This intermediate usually has higher free energy (G) than the substrate. For the reaction to proceed, there has to be an input of energy to overcome this barrier- this is known as the energy of activation (ΔG, or Gibbs energy). This need for energy affects the rate of the reaction; that is, the greater ΔG, the slower the reaction.  Factors Affecting Reaction Velocity If allowed to sit untouched, the flesh of sliced apples will turn brown by a process known as oxidation, caused by an enzyme. If lemon juice is sprinkled on the sliced apple, the vitamin C in the lemon juice will inhibit the formation of this brown color by changing the pH of the environment of the enzyme. Enzyme reactions are affected by reaction conditions such as substrate concentration, pH, temperature, and the presence of inhibitors.  Factors Affecting Reaction Velocity Substrate Concentration Maximal velocity: The rate or velocity of a reaction (v) is the number of substrate molecules converted to product per unit time. The rate of an enzyme- catalyzed reaction increases with substrate concentration until a maximal velocity (Vmax) is reached. At a constant concentration of enzyme, an increase in substrate concentration will cause an increase in the enzyme activity up to the point where the enzyme becomes saturated with substrate. A condition known as steady state is when an enzyme is operating under maximum activity. Factors Affecting Reaction Velocity Temperature Velocity increase with temperature: The reaction velocity increases with temperature until a peak velocity is reached. Velocity decrease with higher temperature: Further elevation of the temperature causes a decrease in reaction velocity as a result of temperature-induced denaturation of the enzyme  Factors Affecting Reaction Velocity pH effect on active site ionization: The concentration of protons ([H+]) affects reaction velocity in several ways. First, the catalytic process usually requires that the enzyme and substrate have specific chemical groups in either an ionized or unionized state in order to interact. pH effect on enzyme denaturation: Extremes of pH can also lead to denaturation of the enzyme. Michaelis-Menten kinetics This diagram illustrates the reaction velocity (v) of a certain enzymatic reaction in relation to its substrate concentration ([S]) in an otherwise stable environment. It yields a solubility curve with an initial steep rise with subsequent plateauing (hyperbolic solubility curve). The maximum reaction velocity (Vmax) is indicated by the plateau phase which is achieved at maximum substrate concentrations. KM is defined as the substrate concentration at which the reaction velocity equals 50% of Vmax. Thanks you!